[2023-06-13 10:52:55,557] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:52:55,559] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:52:55,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c8ba4e7-e141-4db5-ad20-a39ba4853412/dqc_reference
[2023-06-13 10:52:56,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:52:56,827] [INFO] Task started: Prodigal
[2023-06-13 10:52:56,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ec4faaa-9ade-4656-8b86-ac8f2e7e1151/GCA_022708535.1_ASM2270853v1_genomic.fna.gz | prodigal -d GCA_022708535.1_ASM2270853v1_genomic.fna/cds.fna -a GCA_022708535.1_ASM2270853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:53:00,564] [INFO] Task succeeded: Prodigal
[2023-06-13 10:53:00,565] [INFO] Task started: HMMsearch
[2023-06-13 10:53:00,565] [INFO] Running command: hmmsearch --tblout GCA_022708535.1_ASM2270853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c8ba4e7-e141-4db5-ad20-a39ba4853412/dqc_reference/reference_markers.hmm GCA_022708535.1_ASM2270853v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:53:00,765] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:53:00,766] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5ec4faaa-9ade-4656-8b86-ac8f2e7e1151/GCA_022708535.1_ASM2270853v1_genomic.fna.gz]
[2023-06-13 10:53:00,882] [INFO] Query marker FASTA was written to GCA_022708535.1_ASM2270853v1_genomic.fna/markers.fasta
[2023-06-13 10:53:00,882] [INFO] Task started: Blastn
[2023-06-13 10:53:00,883] [INFO] Running command: blastn -query GCA_022708535.1_ASM2270853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c8ba4e7-e141-4db5-ad20-a39ba4853412/dqc_reference/reference_markers.fasta -out GCA_022708535.1_ASM2270853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:53:01,406] [INFO] Task succeeded: Blastn
[2023-06-13 10:53:01,411] [INFO] Selected 10 target genomes.
[2023-06-13 10:53:01,411] [INFO] Target genome list was writen to GCA_022708535.1_ASM2270853v1_genomic.fna/target_genomes.txt
[2023-06-13 10:53:01,415] [INFO] Task started: fastANI
[2023-06-13 10:53:01,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ec4faaa-9ade-4656-8b86-ac8f2e7e1151/GCA_022708535.1_ASM2270853v1_genomic.fna.gz --refList GCA_022708535.1_ASM2270853v1_genomic.fna/target_genomes.txt --output GCA_022708535.1_ASM2270853v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:53:06,054] [INFO] Task succeeded: fastANI
[2023-06-13 10:53:06,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c8ba4e7-e141-4db5-ad20-a39ba4853412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:53:06,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c8ba4e7-e141-4db5-ad20-a39ba4853412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:53:06,057] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:53:06,058] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:53:06,058] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-13 10:53:06,060] [INFO] DFAST Taxonomy check result was written to GCA_022708535.1_ASM2270853v1_genomic.fna/tc_result.tsv
[2023-06-13 10:53:06,061] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:53:06,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:53:06,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c8ba4e7-e141-4db5-ad20-a39ba4853412/dqc_reference/checkm_data
[2023-06-13 10:53:06,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:53:06,083] [INFO] Task started: CheckM
[2023-06-13 10:53:06,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708535.1_ASM2270853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708535.1_ASM2270853v1_genomic.fna/checkm_input GCA_022708535.1_ASM2270853v1_genomic.fna/checkm_result
[2023-06-13 10:53:24,155] [INFO] Task succeeded: CheckM
[2023-06-13 10:53:24,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.58%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:53:24,179] [INFO] ===== Completeness check finished =====
[2023-06-13 10:53:24,179] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:53:24,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708535.1_ASM2270853v1_genomic.fna/markers.fasta)
[2023-06-13 10:53:24,180] [INFO] Task started: Blastn
[2023-06-13 10:53:24,180] [INFO] Running command: blastn -query GCA_022708535.1_ASM2270853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c8ba4e7-e141-4db5-ad20-a39ba4853412/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708535.1_ASM2270853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:53:24,709] [INFO] Task succeeded: Blastn
[2023-06-13 10:53:24,713] [INFO] Selected 10 target genomes.
[2023-06-13 10:53:24,713] [INFO] Target genome list was writen to GCA_022708535.1_ASM2270853v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:53:24,719] [INFO] Task started: fastANI
[2023-06-13 10:53:24,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ec4faaa-9ade-4656-8b86-ac8f2e7e1151/GCA_022708535.1_ASM2270853v1_genomic.fna.gz --refList GCA_022708535.1_ASM2270853v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708535.1_ASM2270853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:53:28,671] [INFO] Task succeeded: fastANI
[2023-06-13 10:53:28,676] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:53:28,676] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_012519885.1	s__JAAYPI01 sp012519885	98.3841	242	266	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__JAAYPI01	95.0	99.15	99.03	0.85	0.70	8	conclusive
--------------------------------------------------------------------------------
[2023-06-13 10:53:28,679] [INFO] GTDB search result was written to GCA_022708535.1_ASM2270853v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:53:28,679] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:53:28,682] [INFO] DFAST_QC result json was written to GCA_022708535.1_ASM2270853v1_genomic.fna/dqc_result.json
[2023-06-13 10:53:28,682] [INFO] DFAST_QC completed!
[2023-06-13 10:53:28,682] [INFO] Total running time: 0h0m33s